Star Trek: Matrix
by Matthew1985
Summary: A crossover between the Matrix and Star Trek: The Next Generation.
1. Unexpected Visit

**Chapter 1:**

**Unexpected Visit**

_Captain's log: Stardate: _308268. _It's been two years since our mission in the Vortex. We have since learned that the Vortex galaxy has been closed to the Federation; but Starfleet feels it may be temporary. The crew has been on shore leave for some time, but reports of the Borg attack in the Sol system does have me worried._

Picard is reading his book in his quarters and a voice calls his title in French: "Mon capitaine!" Picard is startled and puts his book down. "Q! What the hell do you want?" "Well, I thought I'd drop buy and give you a new adventure." "We do not need any of your fantasies, Q. The Federation has had enough!" Q furrows his eyebrows, pretending to be innocent, "Oh, come now, Jean-Luc. I've come to let have a new adventure in a world the Federation has not explored yet." Picard gets a glass of Earl Grey tea and puts it on his table. "What 'world'?" "It's called the Matrix!" "Matrix?" "Yes, you see, they've suffered a lot of losses due to their war with an army of machines called Sentinels. They need your help." "At least you're peaking my interest, Q. Where is this world?" "Earth, actually, early 21st Century, the year 2199 to be exact." "Earth? It'll be good to be home for once." "Yes, but this Earth will not be recognizable. It has only one remaining city called Zion." "Zion?" Picard thinks about this mission. "For once you've peaked my interest. What can you tell me?" "I really don't want to spoil it too much; it's best that you see it for yourself."  
>Q clapped his hands and the <em>Enterprise <em>spun starboard around the nearest sun and went counter clockwise. Picard woke from passing out. "_Bridge to Captain Picard?" _"Yes, Commander, I'm here." "_Are you alright?" _Captain Riker of the Titan asked, "What the Hell happened?" "I just a curious visit from Q. He plunged back in time to the early 21st Century. Mr. Data, what do your instruments say the Enterprise is?" "_Captain, my instruments report that we have been spun around the sun of the nearest system of planets. By calculations, this area of space has no life at all." _"How long til we reach the Sol system?" _"Approx. 6 weeks, sir, at warp speed." "_Proceed, Commander. Keep me apprised when we reach Earth." "_Aye, sir." _

_Captain's log: Supplemental. The Enterprise has been taken backwards in time to the year 2199 and we believe that this Matrix world will be an adventure unlike any other we've experienced before._

"Bridge to Captain Picard, we've reached the Terran system." "Acknowleged, I'm on my way." Picard approaches the Bridge. "Report." "We are entering Earth solar system now, Captain." "Assume standard orbit, Lt. Crusher." "Aye, sir."

Riker approached Picard, 'What did Q say?" Picard responded, "He said that this world has been through a war with Machines. And there's only one city remaining." Riker was a little stunned at this. "Well, I hope it's exciting as he portrayed." "So do I, Number One."


	2. Finding the One

**Chapter 2:**

**Finding the One**

The _Enterprise _arrived at Earth of 2199. "Mr. Data, scan for life-forms." Mr. Data scanned for lifeforms. "Life form counts are inconclusive, Captain." They look around and Mr. Worf got a signal from his tactical station, "Sir, there is a faint signal in the mountainous region." "Mr. Crusher." Wesley stirs the ship to the right. "This signal is intensifying." Data turns in his chair, "The signal is a life-form, human and it is faint." "Mr. Crusher, find a landing area and I'll lead an Away Team to ascertain this. Number One, you have the Bridge." "Aye, sir." "Dr. Crusher, report to Transporter Room 3." "On my way."

Picard and team beam down near where the signal had come from. Data, with tricorder in hand, led the way, "This way, sir." They find a body of a young man. Dr. Crusher kneels down and scans the new patient, "He's alive, but barely." Worf comes from the south and said, "Captain, there is another life-form, a human female, with sever injuries in her torso. No pulse." "It may be too late, Mr. Worf. Beam the deceased to our cargo hold and in a coffin." "Aye, sir." Crusher looked to Picard, "Should we beam him up as well?" "Yes, see if you can raise him." Crusher pushed her combadge, "Crusher to Enterprise, two to beam directly to Sickbay." Crusher and her patient dematerialized. "Mr. Worf, Mr. Data, is it possible to repair this ship?" They looked around and surveyed the damage, "it is possible," Data said, "I'll have Commander LaForge look at it." "Keep me apprised." Picard touched his combadge. "Picard to Bridge, have you found the city?" "_Yes, sir. We have coordinates and we detect human life-signs." "_Acknowleged. One to beam up."


	3. Resurgence

**Chapter 3:**  
><strong>Resurgence<strong>

Picard entered Sickbay and found Dr. Crusher at her office. "How's our patient?" Dr. Crusher rose from her chair, "Alive and there's something you need to see." Picard follows her to the med bed where her patient lies. Beverley tilted the man's side to the side. "I don't know what that is, but it cannot be removed. It appears to be connected to the brainstem." Picard called two officers, Data and LaForge to Sickbay. The two officers arrive. "Mr. Data, can you ascertain what it is?" Data looked at the hole, "It appears to be a socket of some type we have never seen before." LaForge added, "I'll have to get more detail on it. When he wakes, we can ask him." "A socket for what?" Picard asked.  
>"The Matrix," the patient said, who had apparently wakened from the sedative. The patient turned toward his rescuers, "Where am I?" "You are on board a starship, the USS Enterprise. I'm Captain Picard; this is Dr. Crusher, our chief medical officer; Commander Data and Commander LaForge, operations and engineering." Dr. Crusher asked, "What's your name?" The patient answered, "Neo." "Mr. Neo, what's the last thing you remember?" "Fighting Smith."<p> 


	4. Remember

**Chapter 4:**

**Remembering**

Neo tells the Enterprise crew about his past inside and with the Matrix. He informs Picard about his recent battle with the program known as Smith and Zion's efforts to rebuild their home. "We need help." "The Enterprise and her crew are at your disposal to assist you and your crew. We have found your city and are ready to beam down and meet the other survivors. How many people do you suspect are in Zion?" Neo answers, "Hundreds, possibly thousands, Captain." Picard nodded, and touched his combadge, "Mr. Data, is it possible to get a message to Zion?" "_From the information Neo has given us, it is possible to reach them through ships communication systems. There are about 2 ships near Zion within range." _"Mr. Data, Neo here, can you name any ships from your scans?" _"No, not at this time." _"Mr. Data, proceed with communication, irrelevant of which ship answers first. We'll be on the Bridge." "_Aye, sir." _Picard looked around for any comments, with none presented. "Mr. Neo, I'd like you accompany us to our cargo holds. We have put a human female in one of our coffins for burial." "Thank you, Captain. Her name was Trinity." Beverley said, holding his hand, "We're sorry for your loss. She seemed really important." "She was." Neo looks to Picard, "I'm ready to see her." Picard dismisses the meeting.

Neo and Picard go to Cargo Bay 1 and see the coffin, one side open, to see the body of Trinity. "We have to inform you as well that she was pregnant at the time of her death. We are very sorry." "Did you find out the gender?" Beverley joined them, "Too early to tell. I'd say only weeks of pregnancy before her time of death." Neo asked to be alone. "There will be security personnel outside the door waiting to escort you to the Bridge when you're ready. Take your time."

Neo had a moment of silence and remembrance of the woman he loved.


	5. Operator

**Chapter 5:**

"**Operator"**

Mr. Data had worked for 3 hours to find a ship within range of communication. "This is the Starship Enterprise to any ships in the area, please respond." Data looked to Worf, "Nothing yet, sir." Then a voice said, "Operator." "This is Commander Data of the starship Enterprise, to whom am I speaking?" "_Link, operator for the Hammer." _"Mr. Link, we are a Federation starship that has arrived here to assist in the rebuilding of your city. May I speak to the officer in charge?" Picard had approached the Bridge. "We have found a ship, but we have no visual communication." Picard nodded. _"This is Captain Rolland of the Hammer. We ask and request any and all help you can give us. Just make sure you're not out of your own goddamn minds for this assistance. It's been hell here." _"Captain Rolland, this is Captain Picard, we are ready to beam down with some friends of yours that may be among the missing." "We are missing some important crew members of a lot of ships we feel have been lost in our latest war." "We hope to be in assistance, please tell your superiors we're ready to beam down." "_You got it." _"Enterprise out."


	6. Touchdown: Zion

**Chapter 6:**

**Touchdown: Zion**

Captain Jean-Luc Picard and crew beam down to Zion's Temple to ascertain the damage from the recent war with the Machines known as Sentinels. Picard meets Counselor Hamann and the other council members, "Mr. LaForge, my chief engineer, will assess the damage and Mr. Data will assist in repairing your ships. Commander Data is an android, he has studied everything about your ships manifests and your surrounding environment. We have a task back where we come from, and we would like to ask that your ships join us in our fight against a machine-like army known as the Borg." Hamann replies, "I believe that if you help us, we will help you." A figure comes up behind the counselor, "This is Captain Morpheus of the Nebuchanezzer." The two captains shake hands, "I believe I have found someone you lost." Neo walks in front of Picard. "Morpheus." Morpheus embraces Neo and looks at Picard, "How?" "I have a very good doctor." Picard looks behind him and motions a group forward. "I believe you'll want this." Morpheus sees the casket. Looks at Picard. "I'm sorry for you loss, Captain Morpheus. I understand she was a member of your crew." "No." The coffin opens to reveal the body of Trinity. Morpheus becomes emotional, "Thank you for returning her, Captain. You honor us."

"_Worf to Captain_." Picard excuses himself. "Go ahead, Worf." "_Sir, we have found the Nebuchanezzer, sir. She's beyond repair; however, there are several bodies here, all dead. There is one individual Dr. Crusher was able to revive." "_Did you get a name?" _"His name is Tank, sir." _Data approaches, "_Captain, Data here, sir. We've managed to pull apart this vessel piece by piece. We believe that we can construct a new ship called the Nebuchanezzer. I estimate 12 hours of work to complete this task." _"Standby, Picard out." Picard then returns to the group. "Captain Morpheus, we found your lost ship. With your permission, we would like to commission a new ship and call it the Nebuchanezzer in its honor and the honor of your crew." "I would like that very much, but it'll have to be approved by Commander Locke." "May I see him?" Picard meets Commander Locke in his office. "Captain Picard, I've heard of your arrival and your hopes of bringing back the Nebuchanezzer. However, it is out of the question. I do have a question: How the hell did you bring Neo back?" "As I said to Morpheus: I have a good doctors." "And what do you intend to do with my ships?" "Nothing without your approval. However, we are in need of ships. Ships we can make even more powerful by implementing a new system your ships don't have." "And what system would that be?" asked Jason Locke. "Warp drive, sir. It will enable your ships to not only travel through other parts of Earth, but beyond Earth itself. Into space." "Space! We don't have a space program." Counselor Hamann entered the room, "Commander, I believe that Captain has a great idea. He wants to help us rebuild Zion, we should repay him in kind. He has told the Council members about the mysterious species known as Borg and I believe we should help him." "Remember my word, Counselor: Discretion." "And we'll use it, Captain. If you choose not to assist us, you may stay in this office. And if you stay in this office, you relinquish command of Zion's forces to Captains Morpheus and Picard, effective immediately." Jason was infuriated, "You can't do that, sir!" "Correction: I just did." The men leave the office and Hamann tells the guard, "Put Commander Locke in the Stockade until further notice." The guards nodded in obedience. "Thank you , Counselor." "No, Captain Morpheus, thank you." Hamann nods and walks past them.


	7. The Word is Given

**Chapter 7:**

"**The Word is Given"**

Captain Picard orders three damaged ships, the Nebuchanezzer, the Logos and the Hammer, put into the Enterprise's shuttle bays. The captains of those ships, Rolland, Morpheus and Niobe, meet Captain Picard and crew in the Observation Lounge. They discuss the method of aligning the Matrix with the Enterprise's computer and holodeck systems. LaForge's engineering teams works around the clock to repair and install warp drive.

After dismissing the meeting, Picard reports to the Bridge of the Enterprise, while security details escort the guests to their quarters. "Ensign, best speed to Earth's sun and calculate a trajectory for time warp to the 24th Century." "Aye, sir. Estimate 2 minutes to the sun's corona." "Mr. Data, input codes for time warp and engage on my word." Data pressed some buttons. "Coordinates set, trajectory implemented around the sun, in "sling shot" maneuver. Waiting for your word, Captain." Ensign Yeager announces the coordinates are reached, "Mr. Data, Ensign Yeager, as Captain Kirk is fond of saying, 'The word is given.'" The Enterprise sling shots around Earth's sun and makes its way back to the 24th Century. "We've reached the Sol system of the 24th Century, sir." "Mr. Data, scan for Borg cubes." "Scanning." Data's instruments do not detect anything. "Continuing scanning, Data. You have the Bridge, I'll be in the Shuttle 2." "Aye, sir."


	8. Prepare for Battle

**Chapter 8:**

**Prepare for Battle**

Captain's log: Stardate: 68236.2. We've returned to our century and the Enterprise crew is busy making repairs to three ships from the Zion world: The Hammer, the Logos, and the newly commissioned Nebuchanezzer. Our science and engineering crew have work "around the clock" to input the Matrix program through our Holodeck systems. I hope that the program can fit into our system without too much program deletion.

Captain Picard was in the Engineering deck of the ship with Wesley, Geordi and Data. "Sir, we've made a great effort putting the Matrix program through our holodeck program." "That's good, Wesley. Continue." Wesley looked to the Chief Engineer, "Well, sir," Geordi said, "we do have a test that we can perform in here." "In Engineering?" "Yes. Computer, begin Matrix test 1." All of a sudden, the whole engineering deck became green with Latin symbols and kana symbols. "Wow!" Wesley said. "I agree, Mr. Crusher." "It's beautiful, isn't it?" Morpheus came by. "Computer, discontinue simulation." The walls returned to normal. "Captain Morpheus, Commanders Data and LaForge and Lt. Wesley Crusher, one of our brightest young officers." "An honor to meet you. Mr. LaForge, how's my ship coming along?" "It's a work in progress, sir. Would you like to see?" "Yes, please." Data inputted, "I also would like to show the captain our test on Holodeck 3, with your permission, Captain." "At your convenience, Commander."

Morpheus arrives in Shuttlebay 2 for the Nebuchanezzer's refit. "I still remember the outlook. Such precision." "We did have some help." Picard motioned toward an individual. "Tank?" "Captain Morpheus." "I thought you died of your injuries." "Oh, I was dead, but the good doctor Crusher brought me back." Tank looks at the new ship, "Looks beautiful, doesn't she?" "Hm-mm. She does. Let's have a look inside."  
>Geordi explained, "We've replicated the chair designs into our computer system and linked your Matrix program, fully restored of course, to our main ship's computer." "How much power did you use?" Tank asked. Data answered,"Since your system was new to ours, we have to take some power from life-support, but instead, the implementation increased our memory storage by about 20% per ship, so there's 60% extra storage space available. We don't understand how the increase happened, we're just glad it did." Picard asked, "Is there anything we can use that extra storage for?" Data answered, "The holodeck system seemed to be the most logical area of the ship because of all the people that use the Matrix on a daily or weekly basis." Picard nodded his head, "And how is the Holodeck system now?" "The holodeck is more enhanced and up-to-date since last inspection, Captain." "I'll be in the holodeck, Commander LaForge. Mr. Data, let's try out this Matrix system in the Holodeck together." "Aye, sir."<p>

As Picard, Data and Morpheus were walking towards the holodeck, Picard asked him quietly, "Any word about the Borg?" "None as yet, sir. We are still too far out of range to establish contact." "How long til we reach sector 1045?" "5 hours, sir," "Understood, I want to know the instant that we reach the Bassen Rift." Data acknowledged. Picard wanted to meet the fleet at the site of his battle with Shinzon 10 years before, now to actually make it to the Battle Group Omega Fleet. The Bassen Rift would serve as a hiding place until the Borg reach Earth's solar system.

They reach the holodeck and Captains Niobe, Morpheus, Rolland, and operators Tank and Link gather for a meeting before they start simulations. "This is Captain Picard," Morpheus said, "He is Captain of the Enterprise. Any and all orders he gives are to be obeyed. We are here, in this time, to help the Federation fight their most lethal enemy called the Borg. Tank, Link, get back to the ships and prep for simulations." "Aye, sir." Captain Picard touched his combadge, "Computer, transport Mr. Link and Tank to Shuttlebay 2." Picard said. The two operators dematerialize and are beamed to their respective ships. Geordi nodded, "We're ready here, Captain." "Keep this line open at all times, Geordi." "Aye, sir."

They went through simulation after simulation until the frequency was reached. "Captain," Data said, "the link is established." "Begin the first test." "Aye, sir. Computer begin Matrix program." A chair from the Nebuchanezzer appeared. "Captain?" Rolland sat on the chair. "_Please state_ _your name for testing," _the computer said. "Rolland, Captain of the Hammer." _"Voice verification accepted_." Rolland sat himself and relaxed. "Plug in." The needle was locked in. Rolland disappeared, with the chair. A new person was standing. "Captain Rolland?" Picard walked over. Rolland opened his eyes. Another person appeared with Rolland. "Captain," the second man said. "Data?" Picard was surprised. "I am here, sir. I'm in the Construct, the loading program for the Matrix." Picard gave an order,"Computer, show us the Construct." The holodeck turned white. The captain of the Enterprise was looking at a man that sounded like Data but looked human. "How is that possible?" Morpheus had joined the Construct. "Data has told us of his desire to be more human, so the Matrix put that desire into the main database and programmed it as a reality." "_Captain Picard, are you there?" _"Yes, I'm here, Number One. I'm in the Construct, the loading program for the Matrix. Commander, you should see Data." "Mr. Crusher, bring the holodeck area up on the view screen." "One moment, Commander." Riker saw Data the way the Captain saw him. "Where is the real Data?" I'm actually on the main deck of the new Nebuchanezzer, Commander. This is what the Matrix has made me out to be. Since I'm an android, who desires to be human, the program has linked my positronic brain into the Matrix program and thinks of me as human. What you're seeing is what I would look like as a human." Commander Riker and his wife were amazed.

**Holodeck 3**

"Now, can you come from the Construct into the holodeck?" "Yes, Captain, that is the final step." "Mr. Tank, if you please." In a moment, they were back in the holodeck. "That's more like it." Picard touched his badge, "Commander Riker, are you reading us in the holodeck?" "Yes, sir. Along with some holographic images." "I think I can fix that. Computer, can you make the holographic images in the holodeck live people, similar to the Moriarty program?" "Affirmative. " "Enable." The holograms fizzed a bit. Picard touched Rolland's hand and felt it as real. Dr. Crusher examined him. "He's real, Captain. Extraordinary." "Indeed, Doctor."

"Bridge to Captain?" "Go ahead." "Sir, we've reached sector 1045 and we're being hailed by the lead ship." "Admiral DeSoto?" "Yes, sir. He's still has his ship." "On my way."


	9. The Battle Begins

**Chapter 9:**

**The Battle Begins**

The senior officers, with the Zion captains, assembled in the officer's lounge. Captain Riker, USS Titan, began, "I have the space station, DS9, on an open channel." Picard nodded. "Captain Ro, we're honored to have you back in Starfleet." Ro Laren, of the Maquis, smiled back, "It's good to be back, Captain." "We have some friends from the Matrix world here to help us with our fight against the Borg. Are you ready for us?" "Yes, we are. And Captain, Benjamin Sisko has returned from the Celestial Temple." Picard smiled as he saw his friend. "Benjamin." "Captain Picard, Captain Riker, welcome to DS9." "We'll be docking momentarily. Our strike force in the Bassen Rift is on their way, as well. We know the Borg have moved past the Bassen Rift and are heading to Earth, if you can command the Defiant, we can have bring her into the ship and be on board with us." "That is doable, Captain. I also suggest bring Mr. Worf here, with his son, Alexander, who has joined Starfleet." "Alexander, you mean K'mtar?" "No, Captain, the real Alexander. The man you know as K'mtar has vanished. It's a story that even Worf doesn't wish to tell." "I understand. We also hear from the USS Voyager and Captains Kirk, Scott, and Drs McCoy and Bashir and also Vulcan Ambassador Spock is ready to join us in our efforts as well." Sisko was laughing with exhilaration: "This is gonna be one big happy reunion. I do look forward to it." "We'll keep you apprised of our progress, Captain. Picard out!"


	10. Calling of the Guard

**Chapter 10:**

**Calling of the Guard**

Jonathan Archer, Kirk, Montgomery Scott, Chekov, Uhura, Sulu (USS Excelsior); Picard (USS Enterprise-E), Riker (USS Titan), Sisko, Kasidy Yates-Sisko, Worf (USS Defiant) Captain Ezri Dax (USS Aventine), Captains Janeway Chakotay, with about 100 different ships, cruisers and freighters. Some medical ships have arrived in Earth's orbit also. These captains were joined by others: Klingsons: General Martok (IKS Rotarran); Romulans: Tomalok; Vulcans, Andorians, Ferengi: Captain Nog, Bajorans, Trill, and many others that are not named.

All the captains had a meeting with SI (Starfleet Intelligence) to see who will lead the task force against the Borg. Team Alpha is led by Kirk (USS Enterprise-A) Team Beta is led by Picard (USS Enterprise-D) Team Charlie is led by Riker (USS Titan), Team Delta is led by Sisko (USS Defiant) Team Echo is led by Janeway (USS Voyager) and Team Farragut is led by Worf of the Klingon Defense Force, with his son as second officer, under Martok's flag. Team Gamma consists of Neo, Morpheus, Niobe, Rolland, and the Zion ships and crew.

"Captain Picard, we are receiving a hail from the lead Borg cube." "On screen, Mr. Crusher." "WE ARE THE BORG! Lower your shields and surrender your ships. We will add your biological and technological distinctiveness to our own. Your culture will adapt to service us. RESISTANCE is Futile!" Picard put a call on all ships. "All ships, Red Alert. All Hands, Battle Stations. At these coordinates, fire all weapons and retreat when depleted."

The ships and their crews obeyed and many Borg cubes were destroyed, all people resisting assimilation. The Borg Queen called on Picard alter ego, Locutus, but Picard didn't listen. Counselor Troi was there as a guide every step of the way. When the lead Borg cube was destroyed, all of the teams, with all hands on deck, returned to Earth. Many people were commended for their efforts, including the Zion captains and their crew.


	11. Epilogue

**Epilogue**

As the Zion crews and their ships finished repairs, Neo, Morpheus, Niobe returned from the Matrix program. "Thank you, Captains, for your assistance," Picard said. The captains were returned to the Earth of the year 2199. Many captains remained with the Councilors of Zion to continue repairs to Zion and to rebuild other cities lost to the Machines. Eventually, everyone was free of the Matrix. Everyone!  
>The Matrix is real, and in it, you, too, can Live Long and Prosper!<p> 


End file.
